Bolivia's new military government closed the Congress and declared a state of siege throughout the Andean country today, only hours before the State Department announced suspension of U.S economic and military assistance to show displeasure with yesterday's coup.

Bolivia's first democratic government in over a decade was over-thrown by troops of Col. Alberto Natusch Busch, who installed himself as president. Former president Walter Guevara Arze remained in hiding today as a protest strike by the main labor federation proved widely efective.

In Washington, State Department spokesman Tom Reston said the U.S. government "deplores" the change. "Bolivia has taken a step backwards after two years of advance towards democracy," Reston said in explaining the suspension of aid that for this fiscal yer comes to $29 million in economic and military aid.

U.S. officials said that Natusch had been notified of the decision through a third party. These officials also said that the aid cutoff would begin immediately and that, as far as is possible, the assistance would not continue to trickle through the "pipeline," which often means a delay of two or three years before programs actually end. Some $21 million in food aid was not affected.

(Bolivia's new military administration dismissed the U.S. decision to suspend aid, Reuter reported. Guillermo Bedregal, named as foreign minister by Natusch, said the move "will not weigh down the Bolivian economy.

(In a speech at the presidential palace, Natusch rejected threats of economic sanctions as "unacceptable pternalism" and warned that the armed forces would "confront these perils.")

The aid cutoff was the toughest response the Carter administration has yet made to underscore its policy of promoting democratic governments in Latin Americn. Reston said the coup ws "definitely" a setback for that policy "since we support the continuation of the democratic process in Bolivia."

Secretary of State Cyrus Vance, here last week for the opening of the ninth General Assembly of the Organization of American States, held a lunch for Bolivia's top military and civilian leaders during which he made clear that the United States would look with utmost disfavor on a change from civilian to military rule.

U.S. officials in La Paz have been instructed to have no contact with any member of the new government, which today found it necessary to close the recently elected Congress and impose a state of siege after it became clear that the new regime had little popular or political support outside the armed forces.

The Congress was closed this morning after it met last night to pass a resolution unanimously declaring its opposition to the coup and reaffirming its support for Guevara.

In communique, the new military government said its original intention had been to allow the Congress to contiue functioning but that it was being closed because of "repeated calls to subversion by the various political factions" in the parlimentary body.

All of Bolivia's major political coalitions have issued statements opposing the coup although Gen. Hugo Banzer, the military president from 1971 unitl last year -- and the leader of one of three main coalitions at present -- said he supported the new governement "personally and as a member of the armed forces."

Banzer's supporters in the Congress abstained from voting in favor of the resolution last night, while all members of the two other coalitions headed by former presidents Victor Paz Estenssoro and Hernan Siles Zuazo voted in favor.

La Paz remained calm today although almost all business were closed, transportation incuding international flights, was suspended. The country's mines and major industrial plants also were shuttered as a result of the general state.

Members of the Congress were reported meeting in secret, trying to decide what they might do to rally popular support against the Natusch governement, which promised today to respect human and political rights.

Nonetheless, during the first hours after the coup, several radio stations here were "intervened" by soldiers, the university remained closed and a few sporadic bursts of gunfire were heard. There were no reported injuries or deaths today although six were killed yesterday.

There were rumors that factions within the armed forces might attempt a counter coup this weekend. A diplomatic observer said such a move would more likely come "after the dust settles" two to four months from now.